Update app.py

app.py

@@ -1,7 +1,12 @@
 import streamlit as st
 from streamlit_drawable_canvas import st_canvas
 from streamlit_image_coordinates import streamlit_image_coordinates
-
+from idc_index import index
+import os
+import glob
+import shutil
+import dcm2niix
+import subprocess
 
 from model.data_process.demo_data_process import process_ct_gt
 import numpy as np
@@ -15,6 +20,7 @@ import tempfile
 print('script run')
 
 #############################################
+st.session_state.option = None
 # init session_state
 if 'option' not in  st.session_state:
     st.session_state.option = None
@@ -55,12 +61,37 @@ if 'running' not in st.session_state:
 if 'transparency' not in st.session_state:
     st.session_state.transparency = 0.25
 
-case_list = [
-    'model/asset/FLARE22_Tr_0002_0000.nii.gz',
-    'model/asset/FLARE22_Tr_0005_0000.nii.gz',
-    'model/asset/FLARE22_Tr_0034_0000.nii.gz',
-    'model/asset/FLARE22_Tr_0045_0000.nii.gz'
-]
+#download IDC data cases
+client = index.IDCClient()
+#define serieUIDs to download
+serieUIDs_list = ["1.3.6.1.4.1.14519.5.2.1.8421.4008.125612661111422710051062993644",
+                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.552105302448832783460360105045",
+                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.217290429362492484143666931850",
+                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.315023636447426194723399171147",
+                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.307374355712319704057189924161"]
+
+#download series and convert to .nii.gz
+samples_root_dir = "model/asset/idc_samples"
+if not os.path.exists(samples_root_dir) : os.mkdir(samples_root_dir)
+for idx, serieUID_ddl in enumerate(serieUIDs_list):
+  sample_dcm_dir = os.path.join(samples_root_dir, f"ddl_series{idx}_dcm")
+  sample_nii_dir = os.path.join(samples_root_dir, f"ddl_series{idx}_nii")
+  for dir in [sample_dcm_dir, sample_nii_dir]:
+    if os.path.exists(dir):
+      shutil.rmtree(dir)
+    os.makedirs(dir)
+  client.download_from_selection(seriesInstanceUID=\
+     serieUID_ddl, \
+     downloadDir=sample_dcm_dir)
+  subprocess.call(["dcm2niix", "-o", sample_nii_dir, "-z", "y",
+                 "-f", "IDC_%i", "-g", "y", sample_dcm_dir])
+case_list = glob.glob(os.path.join(samples_root_dir, "*nii/*.nii.gz"))
+# case_list = [
+#     'model/asset/FLARE22_Tr_0002_0000.nii.gz',
+#     'model/asset/FLARE22_Tr_0005_0000.nii.gz',
+#     'model/asset/FLARE22_Tr_0034_0000.nii.gz',
+#     'model/asset/FLARE22_Tr_0045_0000.nii.gz'
+# ]
 
 #############################################